Hi
I have tried running a few jobs (~15) on Cufflinks, feature counts and Ht-seq counts. While a few of the jobs were done within an hour, the remaining jobs have been waiting to run for more than 2 days.

Logic: A batch of your jobs will go through, then others that haven't run jobs today will get a batch of their's through, then you will get a batch through, repeat. This helps to share resources fairly among all users. Some people queue up many jobs at time, others just one or two. Each get a "batch" through on each rotation. Deleting/restarting jobs in your account will not change this, except to place the new jobs at the back of the queue, extending wait time even more.

If no jobs at all run within your account, across all of your histories, in any 24-36 hour time period, please let us know. That indicates a problem.